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- PDB-4lub: X-ray structure of prephenate dehydratase from Streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 4lub
TitleX-ray structure of prephenate dehydratase from Streptococcus mutans
ComponentsPutative prephenate dehydratase
KeywordsLYASE / dehydratase / dehydration
Function / homology
Function and homology information


prephenate dehydratase / prephenate dehydratase activity / L-phenylalanine biosynthetic process / cytoplasm
Similarity search - Function
Prephenate dehydratase signature 2. / Prephenate dehydratase, conserved site / Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / Periplasmic binding protein-like II ...Prephenate dehydratase signature 2. / Prephenate dehydratase, conserved site / Prephenate dehydratase / Prephenate dehydratase / Prephenate dehydratase domain profile. / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Prephenate dehydratase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsShin, H.H. / Ku, H.K. / Song, J.S. / Choi, S. / Son, S.Y.
CitationJournal: TO BE PUBLISHED
Title: X-ray structure of prephenate dehydratase from Streptococcus mutans
Authors: Shin, H.H. / Ku, H.K. / Song, J.S. / Choi, S. / Son, S.Y.
History
DepositionJul 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative prephenate dehydratase
B: Putative prephenate dehydratase


Theoretical massNumber of molelcules
Total (without water)62,3592
Polymers62,3592
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-14 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.813, 57.963, 85.051
Angle α, β, γ (deg.)90.00, 125.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-387-

HOH

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Components

#1: Protein Putative prephenate dehydratase


Mass: 31179.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: pheA, SMU_786 / Plasmid: PET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8DUV6, prephenate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 15% polyethylene glycol 8000, 100mM magnesium chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2399 Å
DetectorType: Photonic science VHR CCD / Detector: CCD / Date: Dec 6, 2009
RadiationMonochromator: DMM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2399 Å / Relative weight: 1
ReflectionResolution: 2.097→34.9 Å / Num. all: 25696 / Num. obs: 25692 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 20.97 Å2 / Rmerge(I) obs: 0.0871 / Net I/σ(I): 14.86
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.0871 / Mean I/σ(I) obs: 14.86 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→34.877 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 23.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 1309 5.1 %
Rwork0.19 --
obs0.1915 25655 99.81 %
all-25696 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→34.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 0 228 3259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063132
X-RAY DIFFRACTIONf_angle_d1.2664255
X-RAY DIFFRACTIONf_dihedral_angle_d15.3251121
X-RAY DIFFRACTIONf_chiral_restr0.062488
X-RAY DIFFRACTIONf_plane_restr0.007532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.18410.281300.23712690X-RAY DIFFRACTION100
2.1841-2.28350.23751290.21272697X-RAY DIFFRACTION100
2.2835-2.40390.22041470.19912695X-RAY DIFFRACTION100
2.4039-2.55450.24611400.20552681X-RAY DIFFRACTION100
2.5545-2.75160.22711610.2052675X-RAY DIFFRACTION100
2.7516-3.02840.25441400.1972721X-RAY DIFFRACTION100
3.0284-3.46630.19281690.17732693X-RAY DIFFRACTION100
3.4663-4.36580.1831430.1652717X-RAY DIFFRACTION100
4.3658-34.88190.2281500.19112777X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.2841 Å / Origin y: 13.5826 Å / Origin z: 18.2263 Å
111213212223313233
T0.1491 Å2-0.0045 Å2-0.0195 Å2-0.111 Å20.0084 Å2--0.1234 Å2
L0.5728 °20.2954 °2-0.1353 °2-0.8334 °20.0233 °2--0.4815 °2
S-0.0526 Å °-0.0321 Å °0.0394 Å °-0.1861 Å °0.0663 Å °0.1089 Å °-0.0011 Å °0.0137 Å °-0.0008 Å °
Refinement TLS groupSelection details: ALL

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